[English] 日本語
Yorodumi
- EMDB-1095: A mutant chaperonin with rearranged inter-ring electrostatic cont... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1095
TitleA mutant chaperonin with rearranged inter-ring electrostatic contacts and temperature-sensitive dissociation.
Map dataMap of the E461K mutant of GroEL made from 1477 images picked from 7 cryo micrographs. Big-endian bypte order.
Sample
  • Sample: E461K mutant of GroEL
  • Protein or peptide: E461K mutant of GroEL
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 25.0 Å
AuthorsSewell BT / Best RB / Chen S / Roseman AM / Farr GW / Horwich AR / Saibil HR
CitationJournal: Nat Struct Mol Biol / Year: 2004
Title: A mutant chaperonin with rearranged inter-ring electrostatic contacts and temperature-sensitive dissociation.
Authors: B Trevor Sewell / Robert B Best / Shaoxia Chen / Alan M Roseman / George W Farr / Arthur L Horwich / Helen R Saibil /
Abstract: The chaperonin GroEL assists protein folding through ATP-dependent, cooperative movements that alternately create folding chambers in its two rings. The substitution E461K at the interface between ...The chaperonin GroEL assists protein folding through ATP-dependent, cooperative movements that alternately create folding chambers in its two rings. The substitution E461K at the interface between these two rings causes temperature-sensitive, defective protein folding in Escherichia coli. To understand the molecular defect, we have examined the mutant chaperonin by cryo-EM. The normal out-of-register alignment of contacts between subunits of opposing wild-type rings is changed in E461K to an in-register one. This is associated with loss of cooperativity in ATP binding and hydrolysis. Consistent with the loss of negative cooperativity between rings, the cochaperonin GroES binds simultaneously to both E461K rings. These GroES-bound structures were unstable at higher temperature, dissociating into complexes of single E461K rings associated with GroES. Lacking the allosteric signal from the opposite ring, these complexes cannot release their GroES and become trapped, dead-end states.
History
DepositionSep 1, 2004-
Header (metadata) releaseSep 1, 2004-
Map releaseSep 1, 2005-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025209
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.025209
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1095.gif

Downloads & links

-
Map

FileDownload / File: emd_1095.map.gz / Format: CCP4 / Size: 1001 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of the E461K mutant of GroEL made from 1477 images picked from 7 cryo micrographs. Big-endian bypte order.
Voxel sizeX=Y=Z: 6.67 Å
Density
Contour Level1: 0.017 / Movie #1: 0.025209
Minimum - Maximum-0.0751354 - 0.084824
Average (Standard dev.)-0.000167728 (±0.00857093)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions646464
Spacing646464
CellA=B=C: 426.88 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.676.676.67
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z426.880426.880426.880
α/β/γ90.00090.00090.000
start NX/NY/NZ-96-56-288
NX/NY/NZ192112576
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS646464
D min/max/mean-0.0750.085-0.000

-
Supplemental data

-
Sample components

-
Entire : E461K mutant of GroEL

EntireName: E461K mutant of GroEL
Components
  • Sample: E461K mutant of GroEL
  • Protein or peptide: E461K mutant of GroEL

-
Supramolecule #1000: E461K mutant of GroEL

SupramoleculeName: E461K mutant of GroEL / type: sample / ID: 1000 / Oligomeric state: homo tetradecamer / Number unique components: 1
Molecular weightExperimental: 840 KDa / Theoretical: 840 KDa / Method: sequencing, gel-filtration

-
Macromolecule #1: E461K mutant of GroEL

MacromoleculeName: E461K mutant of GroEL / type: protein_or_peptide / ID: 1 / Name.synonym: E461K / Details: homo tetradecamer / Number of copies: 14 / Oligomeric state: homo tetradecamer / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli) / synonym: E. coli
Molecular weightExperimental: 840 KDa / Theoretical: 840 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)

-
Experimental details

-
Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.84 mg/mL
BufferpH: 7.4 / Details: 20 mM Tris, 5 mM KCl, 10 mM MgCl2, pH 7.4
StainingType: NEGATIVE
Details: grids were flash frozen by plunging into liquid ethane at -170 degrees C. No stain was used.
GridDetails: copper grid, holey carbon films
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Home made plunger
Method: grids were blotted prior to plunging for approximately two seconds

-
Electron microscopy

MicroscopeJEOL 2010HT
Electron beamAcceleration voltage: 200 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsCalibrated magnification: 30000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 30000
Sample stageSpecimen holder: Oxford CT3500 / Specimen holder model: OTHER
TemperatureMin: 100 K / Max: 100 K / Average: 100 K
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 10 µm / Number real images: 7 / Average electron dose: 10 e/Å2
Details: Scanned on a Leafscan 45 at 2540 pixels per inch. Subsequently pixels were averaged in 2x2 blocks.
Bits/pixel: 16

-
Image processing

Final two d classificationNumber classes: 40
Final angle assignmentDetails: Spider euler angles file as follows: 1 3 90.0 90.000 0.00000E+00 2 3 90.0 90.000 3.2143 3 3 90.0 90.000 6.4286 4 3 90.0 90.000 9.6429 5 3 90.0 90.000 12.857 6 3 90.0 90.000 16.071 7 3 90.0 ...Details: Spider euler angles file as follows: 1 3 90.0 90.000 0.00000E+00 2 3 90.0 90.000 3.2143 3 3 90.0 90.000 6.4286 4 3 90.0 90.000 9.6429 5 3 90.0 90.000 12.857 6 3 90.0 90.000 16.071 7 3 90.0 90.000 19.286 8 3 90.0 90.000 22.500 9 3 90.0 90.000 25.714 10 3 90.0 90.000 28.929 11 3 90.0 90.000 32.143 12 3 90.0 90.000 35.357 13 3 90.0 90.000 38.572 14 3 90.0 90.000 41.786 15 3 90.0 90.000 45.000 16 3 90.0 90.000 48.214 17 3 90.0 96.429 0.00000E+00 18 3 90.0 96.429 3.2143 19 3 90.0 96.429 6.4286 20 3 90.0 96.429 9.6429 21 3 90.0 96.429 12.857 22 3 90.0 96.429 16.071 23 3 90.0 96.429 19.286 24 3 90.0 96.429 22.500 25 3 90.0 96.429 25.714 26 3 90.0 96.429 28.929 27 3 90.0 96.429 32.143 28 3 90.0 96.429 35.357 29 3 90.0 96.429 38.572 30 3 90.0 96.429 41.786 31 3 90.0 96.429 45.000 32 3 90.0 96.429 48.214 33 3 90.0 102.857 0.0 34 3 90.0 102.857 6.4825 35 3 90.0 102.857 12.857 36 3 90.0 102.857 19.2885 37 3 90.0 102.857 25.714 38 3 90.0 102.857 32.1425 39 3 90.0 102.857 38.571 40 3 90.0 102.857 45.0
Final reconstructionApplied symmetry - Point group: C7 (7 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Spider
Details: Seven fold symmetry was imposed on the reconstruction.
Number images used: 1477
DetailsSide views only were used in the reconstruction

-
Atomic model buiding 1

Initial modelPDB ID:

1ems

DetailsThe seven membered rings of GroEL (1EMS) were docked separately into the reconstructed density. This was done manually using the programme O.
RefinementProtocol: RIGID BODY FIT

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more